It Doesn't Matter What You Should Have Done
by The Lonely Centurion
Summary: Rated T for character death and just to be safe. With his wife dead, what will happen to Rory Williams. AU. INCOMPLETE
1. Chapter 1

**It Doesn't Matter What You Should Have Done**

First Published – 2011

Original Series broadcast on BBC television  
>Format ©BBC 1963<p>

'Doctor Who' 'TARDIS' etcetera are the trademarks of the British Broadcasting Corporation and are not being used for profit.

All rights reserved. No part of this novel may be reproduced in any form or by any means without prior written consent from the author, except by a reviewer, who may quote brief passages in a review.

This book is a work of fiction. Names, characters, places and incidents are either a product of the author's imagination or used ficticiously. Any resemblance to actual people living or dead, events or locales is entirely coincidental.

Cover Design by TheLonelyCenturion – 2012

This Story Features the Eleventh Doctor as portrayed by Matt Smith, Rory Williams as portrayed by Arthur Darvill, and The Doctor's Daughter Jenny as portrayed by Georgia Moffett

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><p><em>Chapter One<em>

Rory Williams thought to himself, "He always does this, he just acts. He's so impulsive and look where it brought me. He has gotten me killed numerous times and has even erased me from history. Why couldn't he ever think of anyone's safety ever? The Doctor, Amy's Raggedy Doctor. He shows off, he wants everyone to believe that he is so clever, so smart and in control. But he's not, he's a manipulative old man and he's dangerous."

Amy's cries of pain brought him back out of his thoughts and into reality. She was lying on the floor of the TARDIS, and she was so cold and weak. "Doctor do something, this is your fault," Rory screamed, "Help her."

The Doctor looked down at Rory, he saw a desperate man trying to save a dying woman, the most important woman in his life. Solemnly he said, "There's nothing I can do."

Anger flashed through Rory's veins, but seeing his wife begin to cough up blood brought him momentarily out of it. He looked at her and held her hand, "Amy the Doctor's wrong, it's going to be okay," she began to cough up more blood and Rory could see the fear in her eyes. "Amy I love you, you can't leave me," Rory begged.

Weak from internal bleeding she looked up at her husband and said, "I love you Rory Williams." And then she was gone.

"No, no, no, no. Amy! Amy please, remember playing dress up, and our wedding. Amy what about our daughter? I can't do this by myself," pleaded Rory to the corpse of his wife.

The Doctor placed a hand on his shoulder and said, "Rory she's gone. I'm sorry. I'm so sorry."

Rory stood up abruptly and grabbed the Doctor and snarled, "No you're not. This is your fault. It's always your fault. All you ever do is get people hurt." And with that Rory's fist made contact with the time lord's face. The Doctor lay on the ground; his nose was broken and was bleeding. "First you get me killed, you lose my daughter, and then you get my wife killed. Don't you ever think! Or is this all a big game to you Doctor?"

"Rory she was my best friend, I never wanted this to happen."

"Doctor she was my wife and you got her killed. I don't care that you didn't want it to happen. You never want anything bad to happen, but it does. And it's always your fault."

"Rory, I'm sorry okay. I should have been more careful, I should have done more."

"Save it Doctor, it doesn't matter what you should have done. It's what you did do that counted."

"Rory Pond you're right. You're a better man than I'll ever be and you're right about me. I don't think. I just do things without thinking about the consequences. I don't think about how people might get hurt, but they do and it took this to show me."

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><p>Right so this is my first full length story to be published online, and well I've decided to go dark with it. Everyone seems to portray the Doctor as this wonderful person, and trust me I love the show and how he is portrayed, but the doctor is rarely seen as being the bad guy. He is clearly manipulative (watch "The Girl Who Waited" for a perfect example) and is extremely impulsive.<p>

*update: 3/17/11 - just changed the Disclaimer to my new standard disclaimer

_Anyway Please Review, Thanks_


	2. Chapter 2

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction**_

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><p><span>Chapter 2<span>

"_Rory Pond you're right. You're a better man than I'll ever be and you're right about me. I don't think. I just do things without thinking about the consequences. I don't think about how people might get hurt, but they do and it took this to show me,"_ the Doctor said as he slowly began to stand up. Blood was streaming down his face onto his light brown shirt.

Rory paused, and looked at the bloody mess that was the Doctor. He took a deep breath and said, "I finally understand Doctor, I understand why you have so many enemies, why they tried to seal you in the Pandorica, why the Silence wanted you dead. You are the most dangerous man in the universe." Rory paused again before continuing, "Doctor you've always tried to stop the monsters, but you've become the greatest monster."

The Doctor remained silent; the flow of blood coming from his broken nose was slowing down.

Rory looked at the Doctor. He was a shell of the man he pretended to be. Rory then said, "Doctor, just take us home. Take me and Amy's body home." Just then Rory began to break down and cry again, he looked at the Doctor and said, "Take us home now."

"Okay, Rory Williams and Amelia Pond you're going home," the Doctor said solemnly as he flipped a lever on the console. The TARDIS then made its signature sound as it landed in front of the house belonging to Rory Williams.

"Doctor, open the door," Rory said as he knelt to pick up his wife's body. He ran his hand gently through her long ginger hair before picking her up in his arms. As he stood up, he silently looked in the Doctor's eyes. As the Doctor opened the TARDIS doors Rory could see that it was lightly snowing. Rory walked forward into the snowy dusk of his street.

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><p><em>So I'm not exactly sure where this plot is going, which is why this chapter was a bit short. I don't know if I'm going to have the Doctor drop off Rory in the actual world and have Captain JackTorchwood get involved, I might have Rory end up in an alternate reality where Amy is still alive but he has to deal with a second Rory. I also might have him meet the Meta-crisis Doctor or the Doctor's Daughter. I'm pretty much just making the plot up as I go. _

_Thanks For Reading and Please Review_


	3. Chapter 3

_**Disclaimer: Doctor Who is owned by the BBC, this is clearly Fan Fiction**_

Chapter 3

Rory kept walking through the light snow, carrying the body of the woman he loved in his arms. He did not look back until he heard the TARDIS dematerialize. "He's gone," he said no one in particular as he walked through the door of his house into a new life.

Three months had passed and Rory had a new flat and a new job as a Nurse in a London hospital. Rory thought back to how the day after he had been dropped off at his home an American had showed up on his doorstep. He had called himself Captain Jack Harkness and had claimed to be a friend of the Doctor. He said he was head of the Torchwood Institute and could help with the paperwork involve in explaining Amy's death. Three days later a small funeral was held for Amelia Williams at a church not far from their home. The funeral was attended only by close family members, friends, and Captain Jack Harkness.

The moment Captain Harkness approached him after the service would haunt Rory Williams forever.

Harkness said to him, "I know what you've seen and what you've done. You know what's out in the Universe and you know it's dangerous. My team, we fight for humanity. We fight what's in the darkness and we have room for a medic. So do you want the job?"

Rory Williams had looked at the man in disbelief before saying, "This is my wife's funeral and you think it's okay to come here and offer me a job. You're almost as bad as the doctor." Rory had walked away before the American could respond and had never seen him again.

Back in the present Rory's thoughts were interrupted by the sound of a crash coming from his sitting room. "Great," he thought to himself, "stupid cat probably knocked something over." Rory got up and decided to check out the source of the crash. What he found was a bigger surprise than he had expected.

In his sitting room was the remains of lamp his mother had given him, but even stranger was the fact that a blonde girl was picking up the shards.

"Um excuse me," Rory said.

"Hello, sorry about the lamp I'll have it cleaned up in a few minutes," the blonde replied.

"Well okay, but this is my flat. How'd you get in here?"

"Well," she said, "I just used this," showing Rory a brown wristband that he hadn't noticed before.

"That's a Vortex Manipulator," Rory said as he interrupted the pretty young blonde. "Who are you?" he asked.

"I'm Jenny, and who are you that you know what this is?"

"My names Rory and I used to travel a lot," he responded. Rory then asked, "You have a time machine strapped to your wrist and you ended up in my flat. Any reason why?"

_Right, so I went with the return of Jenny plot, but I'm keeping the Torchwood option as an open possibility. Hope you enjoyed the chapter._

_Please Read and Review._


	4. Chapter 4

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 4<span>

"_My names Rory and I used to travel a lot, you have a time machine strapped to your wrist and you ended up in my flat. Any reason why?"_ The words echoed through Jenny's head. She thought to herself, "He travelled a lot? Maybe it was with Dad, maybe he can help me find him?"

"Umm excuse me," Rory said, "I know I might be sounding impatient, but you still haven't answered my question."

"Sorry about that," Jenny said, "But you wouldn't have traveled with the Doctor, have you?"

"Great. Another one of his friends here to ruin everything," responded Rory.

"You know him, well that makes sense that I ended up here then. I was trying to track the TARDIS's energy signature and it led me here. There must be some of it still attached to you," she said.

"Okay well I hope you find the Doctor, so could please get out of my flat and do that," answered Rory.

"I've been trying for years to find him; please you used to travel with him. You must have some way to contact him." Jenny begged.

"Jenny I don't know why you want to find the Doctor and frankly I don't really care," Rory said, "If there is one person in the universe I never want to see again. It's him. He took everything I loved and ruined it. He lost my daughter when she was a newborn, he got her killed as an adult, and then he got my wife killed. Why would I ever want to contact him? Why would you want to find him?"

"Because he's my father," Jenny said.

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><p><em>I'm truly amazed how I can get into such a good writing mood after a smoke, some Tylenol and a nice swim. That combination is just so relaxing. Anyway sorry about the wait in between chapters and the well shortness of this come back chapter. It did have a nice Rory monologue in it though. Anyway I liked it. Well I'll work on prioritizing this story a bit more for you all.<em>

_Please Read, Enjoy, and Review_


	5. Chapter 5

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 5<span>

"He's my father," the words echoed through Rory's ears. He couldn't believe it, the Doctor had never mentioned having any living children. In fact he said that he was the last of his kind, that he was alone and there was no one else like him left in the entire universe.

"I don't believe you," Rory said.

"How can you not believe me?" Jenny asked.

"Well it's pretty easy actually. The Doctor never mentioned you and is the last of his entire species so I really doubt that you're his daughter," responded Rory.

"Fine. I'll prove it to you," said Jenny. She walked up close to Rory and said, "Place your head on my chest."

"What? Jenny I really don't think that would be appropriate," responded a startled Rory.

"You idiot. I'm not asking for you to feel me up, just listen to my hearts beat," said Jenny.

Rory's face got red as he said, "Oh. That would actually make a lot of sense." He then placed his head on the left side of Jenny's chest. He heard the thumping of her heart followed by what sounded like a slight echo.

"Hey you could hurry up, the other heart is on the right side," Jenny said.

"Oh right, sorry," mumbled Rory as he moved his head to his left. He then heard the distinctly separate beating of her second heart. Rory quickly took his head off of the young blonde's bosom and took a step back before he managed to say, "You really do have two hearts."

"Yes that's what I've been trying to tell you, now can you help me find my father?" Jenny said.

Rory thought to himself, "_The Doctor lost Amy and Melody. Does he really deserve my help? No he doesn't, but what about Jenny? She hasn't done anything to me besides break into my flat. She's just a lost girl looking for her family. I have to help her."_ Just as Rory had decided to help his uninvited guest a more pressing matter entered his head.

"I'll try to help you, but first I have to ask you something. Who is your mother?" said Rory.

"Well to be honest, I don't have a mother. I was created out of just my dad's DNA," responded Jenny.

"Oh thank god," said Rory, "I thought you were my grand-daughter for a second."

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><p><em>Yes Rory, putting your head on your grand-daughter's boobs would have been bad. At least Amy is dead in this timeline so you won't have to explain that. Anyway, I'm sorry about the lack of updates for this story. I meant to write this chapter earlier but there was recently a death in my family which prevented me from getting around to any of my stories. Soon I'll be back to my weekend update schedule and I promise I'll write longer chapters. Crap that means I'll probably have to plan out my stories and not just write 'em as I go.<em>


	6. Chapter 6

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter Six<span>

"Oh god no," said Jenny as she laughed. "Do you really think I would have had you do that if you were my grandfather?"

Rory stammered out, "I hope you wouldn't." Then he paused. He looked at the beautiful young woman standing in his living room. She had such an upbeat attitude, but he could see something in her eyes. Behind the mask of this time traveler was a lost little girl who wanted to get home. Rory began to walk across the room to his black leather couch. He sat down and looked back at Jenny before saying, "Why don't you take a seat? I think we're going to have a lot of planning to do."

Jenny gracefully walked over to Rory and sat down. She looked him in the eyes and said, "Yes we do soldier."

The two of them sat and discussed their plans to find the last time lord, Jenny's father, for hours. The two of them brainstormed, argued and revised their plans the entire time. There seemed to be no options for the two travelers. Jenny's Vortex manipulator could only transport one person and even if it could take both of them they still had no idea where or when the Doctor even was.

"Jenny," Rory interrupted as she was about to start on planning another extremely dangerous plan, "I think I know how we can find your Dad and where to get a second manipulator all in one shot."

"How?" Jenny asked.

"Well," Rory began to speak a bit shakily, "I know a man who I promised myself I would never see again. I think we have to contact Torchwood."

"Torchwood?" Jenny said. Then she gasped and said, "You don't mean THE TORCHWOOD, the Captain Jack Harkness Torchwood?"

"That's the one," said Rory.

"I can't believe we have to deal with the intergalactic man whore himself," responded Jenny with a clear sense of disdain.

"Well I don't know about him being a man whore, but I really don't want to deal with him anymore than you do," said Rory. He then leaned back and stared at the ceiling. He mumbled, "Ifdarewaanydotherway," as he began to yawn.

Jenny looked at Rory and for the first time she saw not just a person who could help her find her father, but a man who was broken. She had known that somehow her father was involved with the death of this man's wife and somehow the loss of his daughter. She realized that this man who had lost so much because of her father was still willing to help her, he wasn't broken to her. Well at least not broken beyond repair.

Jenny cleared her mind and said, "Come on I think it's time you get some sleep. We'll finish planning in the morning."

Rory looked at her and stifled another yawn and said, "There's a guest bedroom down on the left if you want to use it."

"Thank you, now get some sleep. You're going to need it tomorrow soldier." Jenny said. She took one last look at him before walking off toward the guest bedroom and thought to herself, "_I think he needs this_." Jenny then took a step back and gave the lonely centurion a kiss on his cheek before walking off to the guest bedroom leaving Rory alone in his living room.

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><p><em>Author's Note:<em>

_Well people this chapter is very long overdue and I hope it will hold you over until well I write another chapter of either of my ongoing stories. I hope you all enjoyed the story "All I've Seen Has Changed My Mind" that I wrote not to long ago. That story originally began as this chapter from the doctors point of view and then became very very different. Just a heads up – I intend to write a sequel or two to that story featuring the "reborn meta-10 doctor" and possibly even a crossover featuring him. (and yes he is a different character, read the story. You'll see.) Anyway I've been rambling but I had posted "All I've…" as a downloadable ebook on my profile but the FBI has shut down megaupload. I'll repost and relink it later or something._

_Also Last Sentence - did you see what I did there?  
><em>


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